One way would be:

>perl -wMstrict -le
"my $s = 'ABC1D A2D D3A foo4bar';
 my @matches = $s =~ m{ A (?: BC)? (\d+) D }xmsg;
 print qq{'$_'} for @matches;
"
'1'
'2'
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Updates:

1. In common with chromatic, I, also, cannot get the OPed code example to work as posted.
   I am going by the first regex in the OP: 'A(BC|)(.*)D'.
2. Slightly altered code example to make results clearer.
3. See the non-capturing grouping expression  (?:pattern) in the Extended Patterns section of perlre.